SMTL ID : 7kel.5 (5 other biounits)

Dihydrodipicolinate synthase (DHDPS) from C.jejuni, H59K mutant with pyruvate bound in the active site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

6 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 3 residues within 4Å: Chain A: Q.140, D.170, C.171 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.140 Hydrogen bonds: A:Q.140 ACT.2: 7 residues within 4Å: Chain A: S.63, A.93, G.94, L.117, S.118, V.119, Y.149 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Water bridges: B:Y.123 Hydrogen bonds: A:A.93, A:G.94, A:V.119 ACT.3: 6 residues within 4Å: Chain A: T.59, Y.149, R.154, K.178, F.260, N.264 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.59 Hydrogen bonds: A:Y.149, A:N.264 Salt bridges: A:R.154 ACT.8: 6 residues within 4Å: Chain A: K.125 Chain B: R.154, F.260, S.263, N.264 Ligands: ACT.9 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.260 Hydrogen bonds: B:N.264 Salt bridges: B:R.154 ACT.9: 7 residues within 4Å: Chain B: Y.149, V.151, R.154, K.178, G.202, N.264 Ligands: ACT.8 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.149, B:N.264 Salt bridges: B:R.154 ACT.10: 5 residues within 4Å: Chain B: I.17, I.18, I.19, D.52, K.88 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.19, B:D.52 Salt bridges: B:K.88

8 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 3 residues within 4Å: Chain A: E.100 Chain B: H.68, E.100 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.95, B:E.100 EDO.5: 5 residues within 4Å: Chain A: L.281, E.282, F.283, C.288, S.289 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.283, A:F.283, A:S.289 EDO.11: 3 residues within 4Å: Chain B: Q.37, R.41, K.44 No protein-ligand interaction detected (PLIP) EDO.12: 9 residues within 4Å: Chain B: E.179, A.180, S.181, G.182, N.183, C.187, E.203, I.206, I.210 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.179, B:S.181, B:G.182, B:N.183, B:N.183 EDO.13: 6 residues within 4Å: Chain B: D.250, E.251, Y.253, N.254, K.304, Y.305 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.253, B:N.254, B:K.304, B:Y.305 EDO.14: 5 residues within 4Å: Chain A: N.96, Y.123 Chain B: S.63, A.64, Y.122 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.96, A:N.96, B:S.63 Water bridges: B:S.63 EDO.15: 6 residues within 4Å: Chain B: L.281, E.282, F.283, L.285, L.287, C.288 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.281, B:F.283, B:L.287 Water bridges: B:S.289 EDO.16: 2 residues within 4Å: Chain B: E.299, K.303 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.303

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.6: 5 residues within 4Å: Chain A: Q.129, Y.132, D.162, T.163, K.166 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.162, A:T.163, A:K.166 Water bridges: A:S.160 PEG.17: 5 residues within 4Å: Chain B: Y.273, L.274, G.276, I.278, E.279 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.274, B:G.276, B:I.278

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.7: 6 residues within 4Å: Chain B: Q.128, Q.129, Y.132, D.162, T.163, K.166 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.166

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yazdi, M.M. et al., Reversing the roles of a crucial hydrogen-bonding pair: a lysine-insensitive mutant of Campylobacter jejuni dihydrodipicolinate synthase, H59K, binds histidine in its allosteric site. To Be Published

Release Date

2021-10-13

Peptides

4-hydroxy-tetrahydrodipicolinate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
J

4-hydroxy-tetrahydrodipicolinate synthase

Related Entries With Identical Sequence